MotionScoreHRpQCT

Motion scoring for HR-pQCT scans using deep convolutional neural networks.

This refactor provides a dataset-first pipeline with BIDS-style derivatives and review-state persistence for direct Slicer integration.

Related repositories:

• Core pipeline (this repo): https://github.com/wallematthias/MotionScoreHRpQCT
• Slicer extension: https://github.com/wallematthias/SlicerMotionScoreHRpQCT

What Changed In v2

• Legacy CLI commands grade and confirm are removed.
• New dataset-driven commands: discover, predict, review-init, review-apply, explain, export.
• Default output structure is now:

<dataset_root>/derivatives/MotionScore/
  index.tsv
  dataset_description.json
  <mirrored-source-path-or-flat-aim-name>/
    predictions/predictions.tsv
    preview/<scan_id>_preview.png
    preview/<scan_id>_slice_profile.png
    review/review.tsv
    review/review.json
    review/review_audit.tsv
    explain/<scan_id>_gradcam.mha

• AIM reading now uses aimio-py.
• Python baseline is now >=3.10.
• Output path mapping:
  • Flat input (*.AIM directly in dataset root): outputs are grouped under folder named after each AIM file stem.
  • Structured input (nested folders): outputs mirror the source folder structure under MotionScore.
• Raw-vs-mask identification:
  • Primary: AIM header processing log (ISQ-origin markers indicate raw images).
  • Fallback: filename-based heuristics when header signal is unavailable.

Installation

conda create -n motionscore python=3.10 -y
conda activate motionscore

# Clone
# git clone <repo-url>
# cd MotionScoreHRpQCT

# Install CLI + torch inference backend
pip install -e ".[torch]"

Models

Use a model registry rooted at --model-root (default ~/.motionscore/MotionScore/models).

Each registered profile points to a directory containing torch checkpoints:

• DNN_0.pt, DNN_1.pt, ... (ensemble members)
• model_registry.json at the model root

Model weights are licensed for usage tracking. In the current deployment configuration, licenses are automatically granted at signup.

CLI Usage

1) Discover scans

motionscore discover /path/to/dataset
motionscore discover /path/to/dataset --json

2) Run prediction + initialize review tables

motionscore predict /path/to/dataset --confidence-threshold 75
# choose a registered model profile
motionscore predict /path/to/dataset --model-id base-v1
# blinded operator training mode
motionscore predict /path/to/dataset --training-mode
# optional: restrict to one scan_id (repeat flag for multiple)
motionscore predict /path/to/dataset --scan-id sub-001_site-tibia_ses-T1_abcdef1234
# optional quick-look PNG controls
motionscore predict /path/to/dataset --preview-panels 5
motionscore predict /path/to/dataset --no-preview-png

Default output root:

/path/to/dataset/derivatives/MotionScore

Optional custom output root:

motionscore predict /path/to/dataset --output-root /tmp/results

3) Update review threshold policy

motionscore review-init /path/to/dataset/derivatives/MotionScore --confidence-threshold 90
# keep/enable blinded operator training mode
motionscore review-init /path/to/dataset/derivatives/MotionScore --training-mode

--confidence-threshold 100 effectively requires review of all scans. When --training-mode is enabled, pending scans are always operator-first and AI prediction is revealed after manual grading.

4) Apply manual review decision for one scan

motionscore review-apply /path/to/dataset/derivatives/MotionScore \
  --scan-id sub-001_site-tibia_ses-T1_abcdef1234 \
  --manual-grade 3 \
  --reviewer mwalle

4b) Clear manual grades for re-review

# clear one operator across all scans
motionscore review-clear /path/to/dataset/derivatives/MotionScore --reviewer opA

# clear everyone
motionscore review-clear /path/to/dataset/derivatives/MotionScore --all-reviewers

5) Generate on-demand Grad-CAM attention map

motionscore explain /path/to/dataset/derivatives/MotionScore \
  --scan-id sub-001_site-tibia_ses-T1_abcdef1234

6) Export final grade table

motionscore export /path/to/dataset/derivatives/MotionScore

Writes motion_grades.tsv at the derivatives root (or custom --output). Export includes current per-scan review state plus machine-readable multi-reviewer summary columns:

• reviewer_count
• reviewers (pipe-delimited reviewer IDs)
• consensus_method (currently mean_manual_grade)
• consensus_mean_manual_grade
• consensus_grade_rounded
• dynamic reviewer slots: reviewer_1_id, reviewer_1_grade, reviewer_2_id, reviewer_2_grade, ...

7) Prepare slice-level retraining manifest (manual labels take priority)

motionscore train-prepare /path/to/dataset/derivatives/MotionScore \
  --output /path/to/dataset/derivatives/MotionScore/training/train_manifest.tsv \
  --slice-count 8 \
  --min-auto-confidence 0.70 \
  --include-auto-without-manual

Training label policy:

• If a manual scan grade exists, it is treated as ground truth and propagated to all slices.
• If no manual grade exists, per-slice auto labels are used (confidence-filtered).
• --slice-count 8 samples eight randomized, spread-out slices per scan (seeded, reproducible).
• Set --slice-count 0 to disable random count sampling and use --slice-step instead.
• train-prepare also builds a slice-wise cache database at training/slice_db/*.npy and records cache_npy_path + cache_index in the manifest so training can load preprocessed slices directly.

8) Transfer-learn from base model weights (PyTorch)

motionscore train \
  --manifest /path/to/dataset/derivatives/MotionScore/training/train_manifest.tsv \
  --model-root ~/.motionscore/MotionScore/models \
  --init-model-id base-v1 \
  --early-stopping-patience 10 \
  --output-model-dir ~/.motionscore/MotionScore/models/knee-v1

Training writes:

• training_metrics.json
• training_plot_live.png (updated every epoch)
• training_plot.png (final summary plot)
• training_plot_model_<n>.png (per-ensemble-model curves)

9) Register and select custom model profiles

motionscore model-register \
  --model-root ~/.motionscore/MotionScore/models \
  --model-id knee-v1 \
  --model-dir ~/.motionscore/MotionScore/models/knee-v1 \
  --display-name "Knee Transfer v1" \
  --domain knee \
  --version v1

motionscore model-list --model-root ~/.motionscore/MotionScore/models

Slicer Integration Contract

This repository is core logic only. A separate Slicer extension should:

1. run motionscore predict ... from a Run button,
2. run motionscore review-apply ... as reviewers step through scans,
3. request motionscore explain ... on demand to overlay Grad-CAM maps,
4. optionally show preview/*_preview.png for quick QC,
5. load all outputs from derivatives without ad hoc state files.

Reference Slicer repository:

• https://github.com/wallematthias/SlicerMotionScoreHRpQCT

Citation

If you use this software, please cite:

Walle, M., Eggemann, D., Atkins, P.R., Kendall, J.J., Stock, K., Müller, R. and Collins, C.J., 2023. Motion grading of high-resolution quantitative computed tomography supported by deep convolutional neural networks. Bone, 166, p.116607. https://doi.org/10.1016/j.bone.2022.116607